AMBER Archive (2005)

Subject: Re: AMBER:how to deal with metal ion?

From: samuel.arey_at_epfl.ch
Date: Fri Dec 30 2005 - 04:56:08 CST

You might try looking at this paper:

UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations
AK Rappe, CJ Casewit, KS Colwell, WA Goddard III, … - J. Am. Chem. Soc, 1992

They attempted to parameterize vdW radii and LJ parameters
for molecular mechanics. In order to make it consistent with
other AMBER vdW radii parameters, you may need to multiply
by a scaling factor (I think it is 0.5) -- look at some AMBER
papers (e.g. Pearlman et al 1995) to double check the scaling
factor.

Sam

Quoting snowyowls <ethercui_at_gmail.com>:

> I using antechamber to deal with a ligand molecular
> there is a calcium ion in this molecular
> i want to using Gaussian to caculate it,useing the key word pop=MK
> but it failed because there is no radius for atom 34 atomic number
> 20
>
> i want to know how to deal with such kind of metal ion,
> can i change it into small atoms,such as Mg?
> or i should try some other programs?
>
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